For the first time, scientists have created from scratch self-assembling protein filaments built from identical protein subunits that snap together spontaneously to form long, helical, thread-like structures.

Protein filaments are important to our bodies. In nature, protein filaments play a key role in cell biology. Such filaments are essential components of:

The cytoskeletons that give cells their shape and ability to move

The cellular microtubules that orchestrate cell division

The most common protein in our bodies, collagen, which gives both strength and flexibility to our bones, cartilage, skin and other tissues.

“Being able to create protein filaments from scratch — or de novo — will help us better understand the structure and mechanics of naturally occurring protein filaments and will also allow us to create entirely novel materials unlike any found in nature,” said David Baker, University of Washington School of Medicine professor of biochemistry and director of the UW Medicine Institute for Protein Design. Baker, who is also a Howard Hughes Medical Institute investigator, was the senior researcher on the project.

Such materials might include man-made fibers that equal or surpass the strength of spider silk, which by weight is stronger than steel, and even nanoscale wire circuits, Baker said.

The designed proteins arrange themsevles into filaments. Image by Ian Haydon/IPD

To design the filaments, the researchers used a computer program developed in the Baker laboratory, called Rosetta, that can predict the shape of a protein from its amino acid sequence. In order to function, proteins must fold into a precise shape. This folding is driven by properties of the individual amino acids and how they interact with each other and the surrounding fluid environment. These forces of attraction and repulsion drive the protein to come to rest in a shape that has the lowest energy level. By calculating which shape that would balance out these forces of attraction and repulsion to yield the lowest total energy level, Rosetta can predict with a high degree of accuracy what shape a protein will assume in nature.

Using Rosetta, the researchers set out to design small proteins that had surface amino acids that would cause them to latch onto each other so that they assembled into a helix, aligning like steps in a winding staircase.For the helix to be stable, the designed protein binds other copies positioned above and below it as the helix wound around, tier on tier.

“We were eventually able to design proteins that would snap together like Legos®,” said Hao Shen, a Ph.D. candidate at the UW Molecular Engineering and Science Institute, who, with Jorge Fallas, an acting instructor in biochemistry, led the study.

Their paper will be published online by the journal Science on Thursday, Nov. 8, 2018.

Fallas said that the designed proteins are relatively small. They are made up of about only 180 to 200 amino acids and measuring only about on nanometer (one billionth of a meter) in length, about the width of 10 hydrogen atoms lined up side by side. They assemble into stable filaments more than 10,000 nanometers long. The researchers also showed that that by tinkering with the designed protein’s concentration in solution and by adding “caps” that inhibited the designs ability to bind, they could drive the filaments to grow or to disassemble.

“The ability to program the dynamics of filament formation will give us insights into how filament assembly and disassembly is regulated in nature,” said Baker. “And the stability of these proteins suggest they could serve as easily modifiable scaffolds for a range of applications ranging from new diagnostic tests to nano-electronics.”